Publications

Identification of monomethyl branched chain lipids by a combination of liquid chromatography tandem mass spectrometry and charge-switching chemistries

Randolph C, Beveridge C, Iyer S, Blanksby S, McLuckey S, Chopra G†

JASMS (2022) 

[JASMS]

Neurotoxic reactive astrocytes induce cell death via saturated lipids

Guttenplan K, Weigel MK, Prakash P, Wijewardhane PR, Hasel P, Rufen-Blanchette U, Münch AE, Blum
JA, Fine J, Neal M, Bruce KD, Gitler AD, Chopra G, Liddelow SA, Barres B.  

Nature (2021) 

[Nature]

[Glia-omics]

[Github]

[ChemRxiv]

[ChemRxiv]

Accurate Prediction of Inhibitor Binding to HIV-1 Protease using CANDOCK

Falls Z, Fine J, Chopra G, Samudrala R.

Fronteirs in Chemistry (2021) 

[Fronteirs in Chemistry]

[ChemBioChem]

Monitoring phagocytic uptake of amyloid β into glial cell lysosomes in real time

Prakash P*, Jethava KP*, Korte N*, Izquierdo P*, Favuzzi E, Rose IVL, Guttenplan KA, Manchanda P, Dutta S, Rochet J-C, Fishell G, Liddelow S, Attwell D, Chopra G†

[Chemical Science]

Graph based machine learning interprets and predicts diagnostic isomer-selective ion-molecule reactions in tandem mass spectrometry.
Fine J, Li JK-Y*, Beck A, Alzarieni K, Ma X, Boulos V, Kenttämaa HI, Chopra G†

Chem. Sci. 11, 11849-11858 (2020).

[Chemical Science]

Accelerated reactivity mechanism and interpretable machine learning model of N-Sulfonylimines towards fast multicomponent reactions
Jethava KP, Fine JA, Chen Y, Hossain A, Chopra G†
Org. Lett. 22, 21, 8480–8486 (2020).

[Organic Letters]

[Reaction Mechanism]

A 2‐Tyr‐1‐Carboxylate Mononuclear Iron Center is the Active Site of Dimethylformamidase
Arya CK, Yadav S, Fine J, Casanal A, Chopra G†, Ramanathan G, Vinothkumar KR, Subramanian R†.

[Angew Chemie. Int. Ed.]

Spectral Deep Learning for Prediction and Prospective Validation of Functional Groups
Fine J, Rasjashekar A*, Jethava K,Chopra G† 

Chem. Sci. 11, 4618-4630 (2020).

Targeting polyamine biosynthesis to stimulate beta cell regeneration in zebrafish
Robertson M ,Padgett L, Fine J, Chopra G, Mastracci T †

Islets. Sep 2;12(5):99-107 (2020).

[ISLETS]

[JCIM]

DUBS: A framework for developing Directory of Useful Benchmarking Sets for virtual screening.
Fine J, Muhoberac M, Fraux G, Chopra G†

J. Chem. Inf. Model. 60, 9, 4137-4143 (2020).

[JCIM]

Shotgun Drug Repurposing Biotechnology to Tackle Epidemics and Pandemics
Mangione W, Falls Z, Melendy T, Chopra G†, Samudrala R†

[Drug Discovery Today]

CANDOCK: Chemical atomic network based hierarchical flexible docking algorithm using generalized statistical potentials 
Fine J, Konc J, Samudrala R, Chopra G†

J. Chem. Inf. Model. 2020, 60, 3, 1509-1527 (2020).

[JCIM]

[BioRxiv]

Graph Neural Networks Bootstrapped for Synthetic Selection and Validation of Small Molecule Immunomodulators
Wijewardhane PR, Jethava KP, Fine JA, Chopra G†

[ChemRxiv]

Computational chemoproteomics to understand the role of selected psychoactives in treating mental health indications 
Fine J, Lackner R, Samudrala R, Chopra G†

Scientific Reports, 9:13155 (2019).

[Scientiffic Reports]

Integrated pan-cancer map of EBV-associated neoplasms reveals functional host-virus interactions
Chakravorty S, Yan B, Wang C, Wang L, Quaid JT, Lin CF, Briggs SD, Majumder J, Canaria DA, Chauss D, Chopra G, Olson MR, Zhao B, Afzali B, Kazemian M

Rapid, Refined, and Robust Method for Expression, Purification, and Characterization of Recombinant Human Amyloid-beta M1-42 
Prakash P, Lantz TC, Jethava K, Chopra G†

Methods Protoc. 2019, 2(2), 48 (2019).

Lemon: a framework for rapidly mining structural information from the Protein Data Bank 
Fine J, Chopra G†

Bioinformatics, 35(20): 4165–4167 (2019).

DOI: btz178

Molecular Interactions Using New Technology: A Virtual Reality Gaming Platform to Visualize and Manipulate Molecules
Zhang W, Fine J*, Sculley C, McGraw J, Chopra G†

[ChemRxiv] [YouTube] [Abstract]

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 
Keasar C, McGuffin LJ, Wallner B, Chopra G, et. al.

Scientific Reports, 2018, 8:9939 (2018).

Inhibition of 12/15-lipoxygenase protects against ß cell oxidative stress and glycemic deterioration in mouse models of type 1 diabetes.
Hernandez-Perez M, Chopra G, Fine J, Conteh AM, Anderson RM, Linnemann AK, Benjamin C,
Nelson JB, Benninger KS, Nadler JL, Maloney DJ, Tersey SA, Mirmira RG.
Diabetes, 2017, [Epub ahead of print] 
PMID: 28842399

Aminoisoquinoline benzamides, FLT3 and Src-family kinase inhibitors, potently inhibit proliferation of acute myeloid leukemia cell lines
Larocque E, Naganna N, Ma X, Opoku-Temeng C, Carter-Cooper B, Chopra G, Lapidus RG, Sintim HO.
Future Med Chem, 2017, 9(11), 1213-1225
PMID:28490193

Identification of new FLT3 inhibitors that potently inhibit AML cell lines, via an azo click-it/staple-it approach
Zhou J, Ma X, Wang C, Carter-Cooper B, Larocque, E, Fine J,
Tsuji G, Yang F, Chopra G, Lapidus RG, Sintim HO*.
ACS Med Chem Lett, 2017, 8 (5), 492–497
PMID: 28523099

[PDF]

Combating Ebola with Repurposed Therapeutics Using the CANDO Platform
Chopra G†, Kaushik S, Elkin PL, Samudrala R
Molecules, 2016, 21(12): 1537
PMID:27898018

[PDF]

Summary: With the use of the CANDO platform and in vitro data, a significant reduction in time, risk, cost, and resources was shown when identifying drug leads for future Ebola outbreaks compared to tradition methods.

CD28 Costimulation: From Mechanism to Therapy
Esensten JH, Helou YA, Chopra G, Weiss A, Bluestone JA
Immunity, 2016, 44(5): 973-988
PMID: 27192564

[PDF]

Summary: This paper summarizes the current understanding of complex costimulatory pathways, including the individual roles of the CD28, B7-1/CD80, and B7-2/CD86 molecules.

Exploring polypharmacology in drug discovery and repurposing using the CANDO platform
Chopra G†, Samudrala R
Current Pharmaceutical Design, 2016, 22(21):3109-23
PMID: 27013226

[PDF]

Summary: Shows how the CANDO platform can be used to analyze and determine the contribution of multitargeting based approach (polypharmacology) to drug repurposing.

Divergent phenotypes of human regulatory T cells expressing the receptors TIGIT and CD226
Fuhrman CA, Yeh W-I, Seay HR, Lakshmi PS, Chopra G, Zhang L, Perry DJ, McClymont SA, Yadav M, Lopez MC, Baker HV, Zhang Y, Li Y, Whitley M, von Schack D, Atkinson MA, Bluestone JA, Brusko TM
Immunology, 2015, 195(1): 145-155
PMID: 25994968

[PDF]

Summary: A set of studies elucidating functionally distinct regulatory T-cell subsets that may help direct cellular therapies and provide important phenotypic markers for assessing the role of Tregs in health and disease.

Multiscale modeling of relationships between protein classes and drug behavior across all diseases using the CANDO platform
Sethi G*, Chopra G*, Samudrala R
Medicinal Chemistry, 2015, 15(8): 705-17
PMID: 25694071

[PDF]

Summary: Uses the CANDO platform to analyze the interaction signatures between human approved compounds and the druggable proteome to determine drug behavior for different indications/diseases.

The chromatin-modifying enzyme Ezh2 is critical for the maintenance of regulatory T-cell identity
DuPage M, Chopra G, Quiros J, Rosenthal WL, Morar MM, Holohan D, Zhang R, Turka L, Marson A, Bluestone JA
Immunity, 2015, 42(2): 227-38
PMID: 25680271

[PDF]

Summary: Chromatin-modifying enzyme along with CD28 costimulation are crucial for the maintenance of Treg cell identity during cellular activation.

Oxido-reductive regulation of human vascular remodeling by the orphan receptor tyrosine kinase ROS1
Ali Za, de Jesus Perez V, Yuan K, Orcholski M, Pan S, Qi W, Chopra G, Adams C, Kojima Y, Leeper NJ, Qu X, Zaleta-Rivera K, Kato K, Yamada Y, Oguri M, Kuchinsky A, Channon K, Charest A, Quertermous T, Ashley EA
J. Clinical Investigation, 2014, 124(12): 5159-74
PMID: 25401476

[PDF]

Summary: This study indicates that glutathione peroxidase-1 (GPX1)-dependent alterations in oxido-reductive stress promote ROS1 activation and mediate vascular remodeling.

CANDO and the infinite drug discovery frontier
Minie ME*, Chopra G*, Sethi G, Horst JA, Roy A, White G, Samudrala R
Drug Discovery Today, 2014, 19(9):1353-63
PMID: 24980786

[PDF]Summary: The Computational Analysis of Novel Drug Opportunities (CANDO) platform (http://protinfo.org/cando) uses similarity of compound-proteome interaction signatures to infer homology of compound/drug behavior.

WeFold: Large-scale Coopetition for Protein Structure Prediction
Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, et. al.
Proteins, 2014, 82(9):1850-1868
PMC:4249725

[PDF]

Summary: This manuscript describes both successes and areas needing improvement as identified throughout the first WeFold experiment and discusses the efforts that are underway to advance this initiative.

Distal effect of amino acid substitutions in CYP2C9 polymorphic variants causes differences in interatomic interactions against (S)-warfarin
Lertkiatmongkol P, Assawamakin A, White G, Chopra G, Rongnoparut P, Samudrala R, Tongsima S
PLoS One, 2013, 8(9): e74053
PMID: 24023924

[PDF]

Strategic protein target analysis for developing drugs to stop dental caries
Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JDB
Adv. Dent. Res., 2012, 24(2): 86-93
PMID: 22899687

[PDF]

Summary: The entire Streptococcus mutans proteome was analyzed for potential drug targets by investigating their uniqueness with respect to non-cariogenic dental plaque bacteria, quality of protein structure models, and the likelihood of finding a drug for the active si

KOBAMIN – KnOwledge BAsed MINimization server for protein structure refinement
Rodrigues J, Levitt M and Chopra G†
Nucleic Acid Research, 2012, Web Server Issue. 40 (W1): W323-W328
PMCID: PMC3394243

[PDF]

Summary: The KoBaMIN web server provides an online interface to a simple, consistent and computationally efficient protein structure refinement protocol based on minimization of a knowledge-based potential of mean force.

Remarkable patterns of surface water ordering around polarized buckminsterfullerene
Chopra G† and Levitt M
Proc. Natl. Acad. Sci. U.S.A., 2011, 108(35):14455-14460
PMID: 21844369

[PDF]

Summary: Molecular Dynamics simulations using a state-of-the-art quantum mechanical polarizable force field (QMPFF3) shows that polarization increases ordered water structure so that the imprint of the hydrophobic surface atoms on the surrounding waters is stronger and extends to long-range.

Consistent refinement of submitted models at CASP using a knowledge-based potential
Chopra G†, Kalisman N, Levitt M
Proteins, 2010, 78(12): 2668-2678
PMC2911515

[PDF]

Solvent dramatically affects protein structure refinement
Chopra G, Summa CM, Levitt M
Proc. Natl. Acad. Sci. U.S.A., 2008, 105(51): 20239-20244
PMID: 19073921

[PDF]